From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Sep 30 2011 - 08:06:26 CDT
andres,
this kind of thing has been discussed to death on this list.
you cell is shrinking too much, so that the domain
decomposition needs to be re-initialized.
just split your trajectory into multiple segments.
axel.
On Fri, Sep 30, 2011 at 12:52 AM, Andres Morales N
<andresmoralesn2_at_hotmail.com> wrote:
>
> Dear NAMD Users:
>
> I am working with a dppc lipid bilayer with a cationic peptid in water. I
> built the system using preequilibrated dppc bilayer and peptide (they both
> were equilibrated separately). Dppc+water and peptide pdb file were merged
> taking care of appropriate orientation and position for the peptide.
> Overlapping water molecules were deleted using:
>
> set del1 [atomselect $dppc_bact "water and same residue as {water and within
> 2 of protein}"]
> set seg1 [$del1 get segid]
> set res1 [$del1 get resid]
> set name1 [$del1 get name]
> for {set i 0} {$i < [llength $seg1]} {incr i} {
> delatom [lindex $seg1 $i] [lindex $res1 $i] [lindex $name1 $i]
> }
> writepsf bact_dppc_temp1.psf
> writepdb bact_dppc_temp1.pdb
>
>
> Finally the system was ionized in order to get a cero net charge.
>
>
> The system was equilibrated (NPT ensemble) directly using files obtained
> with the process mentioned above, but the following error appeared during
> the process:
>
> FATAL ERROR: Periodic cell has become too small for original patch grid!
> Possible solutions are to restart from a recent checkpoint,
> increase margin, or disable useFlexibleCell for liquid simulation.
> [0] Stack Traceback:
> [0] _ZN9HomePatch14positionsReadyEi+0x6e [0x8404a6e]
> [1] _ZN9Sequencer17runComputeObjectsEii+0xc3 [0x8491eb3]
> [2] _ZN9Sequencer9integrateEv+0x1074 [0x848ed88]
> [3] _ZN9Sequencer9algorithmEv+0x327 [0x848bd7b]
> I also tried another method: Minimization (20000 steps), heating to 300 K
> (20000 step) and equilibration (1 ns). I had no problems neither at system
> minimization nor at system heating. But
> when I was running sytem equilibration it appeared thesame mistake: FATAL
> ERROR: Periodic cell has become too small for original patch grid!
>
> I have tried some solutions:
>
> 1) I increased margin to 1, 2, 3, 5 and 8
> 2) Also I disabled useFlexibleCell in the simulation
>
> But none of them worked.
>
> Also I looked at dcd output file using VMD and there is nothing unusual
> inthe vizualization. I checked the log output file and there is no
> critical increasing or decriasing of energy. It seems a pretty normal
> equilibrationprocess.
>
> I used the following configuration file for the equilibration:
> structure bact_dppc_90_1.psf
> coordinates bact_dppc_90_1.pdb
> bincoordinates bact_dppc_90_1_cal300.coor
> binvelocities bact_dppc_90_1_cal300.vel
> set outputname bact_dppc_90_1_eq
> firsttimestep 0
> paraTypeCharmm on
> parameters par_lipid27.rtf
> parameters par_all27_prot_lipid.prm
> exclude scaled1-4
> 1-4scaling 1.0
> cutoff 12.
> switching on
> switchdist 8.
> pairlistdist 13.5
> margin 2.5
>
> timestep 1.0 ;# 1fs/step
> rigidBonds all ;# needed for 1fs steps
> nonbondedFreq 1
> fullElectFrequency 2
> stepspercycle 20
>
> #PME (for full-system periodic electrostatics)
> PME yes
> PMEGridSizeX 100
> PMEGridSizeY 80
> PMEGridSizeZ 84
> # Constant Temperature Control
> langevin on ;# do langevin dynamics
> langevinDamping 5 ;# damping coefficient (gamma) of 1/ps
> langevinTemp 300
> langevinHydrogen off ;# don't couple langevin bath to hydrogens
>
> # Constant Pressure Control (variable volume)
> useGroupPressure yes ;# needed for 2fs steps
> useFlexibleCell no ;# no for water box, yes for membrane
> useConstantArea no ;# no for water box, yes for membrane
> langevinPiston on
> langevinPistonTarget 1.01325 ;# in bar -> 1 atm
> langevinPistonPeriod 200.
> langevinPistonDecay 50.
> langevinPistonTemp 300
>
> # Output
> outputName $outputname
> dcdfreq 1000
> outputEnergies 100
> # Boundary conditions
> extendedSystem bact_dppc_90_1_cal300.xsc
> wrapWater on
> wrapAll on
> # Restrains
> fixedAtoms on
> fixedAtomsFile dppc_bact_90_1_restr.pdb ### Three atoms (CA of three
> aminoacids)positionswere restrained in order to forbid peptid motion
> during equilibration
> fixedAtomsCol B
> fixedAtomsForces on
> # Equilibracin
> run 1000000
>
>
>
>
>
> I wait someone could help me with some solution.
>
>
> Thank a lot.
>
>
> Hernn Andrs Morales Navarrete
>
> Biophysics and Molecular Modeling Group
> Physics Department
> Escuela Politcnica Nacional, Quito - Ecuador
> Ladrn de Guevara E11-253.
> Casilla 17-01-1253
> http://www.ciencias.epn.edu.ec/~biomod/
>
>
-- Dr. Axel Kohlmeyer akohlmey_at_gmail.com http://goo.gl/1wk0 Institute for Computational Molecular Science Temple University, Philadelphia PA, USA.
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:20:52 CST